[gmx-users] Re: Fluctuations in NVT and NPT resulting plots
jalemkul at vt.edu
Sun Oct 21 16:22:54 CEST 2012
On 10/21/12 8:21 AM, Ali Alizadeh wrote:
> Dear Justin
> It is true that we can not get profile volume vs. time(only nvt
> step), but after that we performed production md, we can
> illustrate profile density and volume profile vs. time. However we
> cannot get constant volume!
> Do I mistake? If it is possible , You can explain more about that fluctuation?
If the ensemble is NPT during the production run, then the box volume is not
constant. Pressure is constant (on average) and thus the box vectors will
fluctuate in response to the pressure coupling algorithm scaling the vectors.
If you are unclear on how this works, then please refer to the primary
literature for the pressure coupling algorithm you are using to understand what
it is doing.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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